Selecting ribosomal protein genes for invertebrate phylogenetic inferences: How many genes to resolve the Mollusca?

Methods in Ecology and Evolution

Volumn 2, Issue 1, 2011, Pages 34-42

  Meyer, Achim ^a   Witek, Alexander ^a   Lieb, Bernhard ^a  

^a JOHANNES GUTENBERG UNIVERSITY   (Germany)

Author keywords

EST; Gene selection; Mollusca; Phylogenomics; Ribosomal proteins; Taxon sampling

Indexed keywords

EID: 80053133022     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/j.2041-210X.2010.00052.x     Document Type: Article

References (66)

1. Aguileta, G., Marthey, S., Chiapello, H., Lebrun, M.-H., Rodolphe, F., Fournier, E., Gendrault-Jacquemard, A. & Giraud, T. (2008) Assessing the performance of single-copy genes for recovering robust phylogenies. Systematic Biology, 57, 613-627.
2. Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402.
3. Balasubramanian, S., Zheng, D., Liu, Y.-J., Fang, G., Frankish, A., Carriero, N., Robilotto, R., Cayting, P. & Gerstein, M. (2009) Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biology, 10, R2.
4. Bergsten, J. (2005) A review of long-branch attraction. Cladistics, 21, 163-193.
5. Birney, E., Clamp, M. & Durbin, R. (2004) GeneWise and Genomewise. Genome Research, 14, 988-995.
6. Blanquart, S. & Lartillot, N. (2006) A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution. Molecular Biology and Evolution, 23, 2058-2071.
7. Bleidorn, C., Podsiadlowski, L., Zhong, M., Eeckhaut, I., Hartmann, S., Halanych, K. & Tiedemann, R. (2009) On the phylogenetic position of Myzostomida: can 77 genes get it wrong? BMC Evolutionary Biology, 9, 150.
8. Bourlat, S.J., Juliusdottir, T., Lowe, C.J., Freeman, R., Aronowicz, J., Kirschner, M., Lander, E.S., Thorndyke, M., Nakano, H., Kohn, A.B., Heyland, A., Moroz, L.L., Copley, R.R. & Telford, M.J. (2006) Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature, 444, 85-88.
9. Brochier, C., Philippe, H. & Moreira, D. (2000) The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends in Genetics, 16, 529-533.
10. Burleigh, J.G., Driskell, A.C. & Sanderson, M.J. (2006) Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets. Systematic Biology, 55, 426-440.
11. Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17, 540-552.
12. Collins, T.M., Fedrigo, O. & Naylor, G.J.P. (2005) Choosing the best genes for the job: the case for stationary genes in genome-scale phylogenetics. Systematic Biology, 54, 493-500.
13. Dudov, K.P. & Perry, R.P. (1984) The gene family encoding the mouse ribosomal protein L32 contains a uniquely expressed intron-containing gene and an unmutated processed gene. Cell, 37, 457-468.
14. Dunn, C.W., Hejnol, A., Matus, D.Q., Pang, K., Browne, W.E., Smith, S.A., Seaver, E., Rouse, G.W., Obst, M., Edgecombe, G.D., Sorensen, M.V., Haddock, S.H., Schmidt-Rhaesa, A., Okusu, A., Kristensen, R.M., Wheeler, W.C., Martindale, M.Q. & Giribet, G. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature, 452, 745-749.
15. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with improved accuracy and speed. Computational Systems Bioinformatics Conference, Proceedings, 2004IEEE, 728-729.
16. Gatesy, J., DeSalle, R. & Wahlberg, N. (2007) How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence Systematic Biology, 56, 355-363.
17. Giribet, G., Distel, D.L., Polz, M., Sterrer, W. & Wheeler, W.C. (2000) Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and morphology. Systematic Biology, 49, 539-562.
18. Goddard, W., Kubicka, E., Kubicki, G. & McMorris, F.R. (1994) The agreement metric for labeled binary-trees. Mathematical Biosciences, 123, 215-226.
19. Goldman, N. (1998) Phylogenetic information and experimental design in molecular systematics. Proceedings of the Royal Society of London, Series B: Biological Sciences, 265, 1779-1786.
20. Graybeal, A. (1994) Evaluating the phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates. Systematic Biology, 43, 174-193.
21. Graybeal, A. (1998) Is it better to add taxa or characters to a difficult phylogenetic problem? Systematic Biology, 47, 9-17.
22. Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
23. Haszprunar, G. (2000) Is the Aplacophora monophyletic? A cladistic point of view. American Malacological Bulletin, 15, 115-130.
24. Haszprunar, G., Schander, C. & Halanych, K.M. (2008) Relationships of Higher Molluscan Taxa. University of California Press, Berkley, Los Angeles, London.
25. Hausdorf, B., Helmkampf, M., Meyer, A., Witek, A., Herlyn, H., Bruchhaus, I., Hankeln, T., Struck, T.H. & Lieb, B. (2007) Spiralian phylogenomics supports the resurrection of Bryozoa comprising Ectoprocta and Entoprocta. Molecular Biology and Evolution, 24, 2723-2729.
26. Hejnol, A., Obst, M., Stamatakis, A., Ott, M., Rouse, G.W., Edgecombe, G.D., Martinez, P., Baguñà, J., Bailly, X., Jondelius, U., Wiens, M., Müller, W.E.G., Seaver, E., Wheeler, W.C., Martindale, M.Q., Giribet, G. & Dunn, C.W. (2009) Assessing the root of bilaterian animals with scalable phylogenomic methods. Proceedings of the Royal Society of London, Series B: Biological Sciences, 276, 4261-4270.
27. Heywood, V.H. (1995) Global Biodiversity Assessment: Published for the United Nations Environment Programme. Cambridge University Press, Cambridge, UK.
28. Jobb, G., von Haeseler, A. & Strimmer, K. (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evolutionary Biology, 4, 18.
29. Keane, T.M., Naughton, T.J. & McInerney, J.O. (2007) MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. Nucleic Acids Research, 35, W33-W37.
30. Kenmochi, N., Kawaguchi, T., Rozen, S., Davis, E., Goodman, N., Hudson, T., Tanaka, T. & Page, D. (1998) A map of 75 human ribosomal protein genes. Genome Research, 8, 509-523.
31. Konstantinidis, K.T., Ramette, A. & Tiedje, J.M. (2006) Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Applied Environmental Microbiology, 72, 7286-7293.
32. Kuramae, E., Robert, V., Echavarri-Erasun, C. & Boekhout, T. (2007) Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom. BMC Evolutionary Biology, 7, 134.
33. Kuzumaki, T., Tanaka, T., Ishikawa, K. & Ogata, K. (1987) Rat ribosomal protein L35a multigene family: molecular structure and characterization of three L35a-related pseudogenes. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, 909, 99-106.
34. Lartillot, N. & Philippe, H. (2004) A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Molecular Biology and Evolution, 21, 1095-1109.
35. Leigh, J.W., Susko, E., Baumgartner, M. & Roger, A.J. (2008) Testing congruence in phylogenomic analysis. Systematic Biology, 57, 104-115.
36. Lieb, B. & Todt, C. (2008) Hemocyanin in mollusks-A molecular survey and new data on hemocyanin genes in Solenogastres and Caudofoveata. Molecular Phylogenetics and Evolution, 49, 382-385.
37. Lindberg, D.R., Ponder, W.F. & Haszprunar, G. (2004) The Mollusca: Relationships and Patterns from their First Half-Billion Years. Oxford University Press, Oxford.
38. Marygold, S., Roote, J., Reuter, G., Lambertsson, A., Ashburner, M., Millburn, G., Harrison, P., Yu, Z., Kenmochi, N., Kaufman, T., Leevers, S. & Cook, K. (2007) The ribosomal protein genes and Minute loci of Drosophila melanogaster. Genome Biology, 8, R216.
39. Meyer, A., Todt, C., Mikkelsen, N. & Lieb, B. (2010) Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity. BMC Evolutionary Biology, 10, 70.
40. Nakao, A., Yoshihama, M. & Kenmochi, N. (2004) RPG: the Ribosomal Protein Gene database. Nucleic Acids Research, 32, D168-170.
41. Nesnidal, M.P., Helmkampf, M., Bruchhaus, I. & Hausdorf, B. (2010) Compositional heterogeneity and phylogenomic inference of metazoan relationships. Molecular Biology and Evolution. doi: 10.1093/molbev/msq097.
42. Nye, T.M.W., Lio, P. & Gilks, W.R. (2006) A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics, 22, 117-119.
43. Passamaneck, Y.J., Schander, C. & Halanych, K.M. (2004) Investigation of molluscan phylogeny using large-subunit and small-subunit nuclear rRNA sequences. Molecular Phylogenetics and Evolution, 32, 25-38.
44. Penny, D. & Hendy, M.D. (1985) The use of tree comparison metrics. Systematic Zoology, 34, 75-82.
45. Perina, D., Cetkovic, H., Harcet, M., Premzl, M., Lukic-Bilela, L., Muller, W.E. & Gamulin, V. (2006) The complete set of ribosomal proteins from the marine sponge Suberites domuncula. Gene, 366, 275-284.
46. Peterson, K.J. & Eernisse, D.J. (2001) Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences. Evolution and Development, 3, 170-205.
47. Philippe, H. & Telford, M.J. (2006) Large-scale sequencing and the new animal phylogeny. Trends in Ecology & Evolution, 21, 614-620.
48. Philippe, H., Derelle, R., Lopez, P., Pick, K., Borchiellini, C., Boury-Esnault, N., Vacelet, J., Renard, E., Houliston, E., Quéinnec, E., Da Silva, C., Wincker, P., Le Guyader, H., Leys, S., Jackson, D.J., Schreiber, F., Erpenbeck, D., Morgenstern, B., Wörheide, G. & Manuel, M. (2009) Phylogenomics revives traditional views on deep animal relationships. Current Biology, 19, 706-712.
49. Pojeta, J., Jr. & Runnegar, B. (1976) The Paleontology of Rostroconch Mollusks and Early History of the Phylum Mollusca. US Department of the Interior, US Geological Survey (Reston, VA), Washington, DC.
50. Regier, J.C., Shultz, J.W., Zwick, A., Hussey, A., Ball, B., Wetzer, R., Martin, J.W. & Cunningham, C.W. (2010) Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature, 463, 1079-1083.
51. Robinson, D.F. & Foulds, L.R. (1981) Comparison of phylogenetic trees. Mathematical Biosciences, 53, 131-147.
52. Roeding, F., Hagner-Holler, S., Ruhberg, H., Ebersberger, I., von Haeseler, A., Kube, M., Reinhardt, R. & Burmester, T. (2007) EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Molecular Phylogenetics and Evolution, 45, 942-951.
53. Salvini-Plawen, L.v. (1980) A reconsideration of systematics in the Mollusca (Phylogeny and higher classification). Malacologia, 19, 249-278.
54. Shimodaira, H. & Hasegawa, M. (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114-1116.
55. Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690.
56. Steinke, D., Salzburger, W. & Meyer, A. (2006) Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs. Journal of Molecular Evolution, 62, 772-784.
57. Sugiura, N. (1978) Further analysts of the data by Akaike's information criterion and the finite corrections. Communications in Statistics - Theory and Methods, 7, 13-26.
58. Swofford, D. (2003) PAUP. Phylogenetic Analysis Using Parsimony (and other methods), Version 4. Sinauer Associates, Sunderland, Massachusetts.
59. Todt, C., Okusu, A., Schander, C. & Schwabe, E., 2008. Phylogeny of Solenogastres, Caudofoveata and Polyplacophora. Phylogeny and Evolution of the Mollusca (eds W.F. Ponder & D.R. Lindberg), pp. 71-96. University of California Press, Berkley, Los Angeles, London.
60. Townsend, J.P. (2007) Profiling phylogenetic informativeness. Systematic Biology, 56, 222-231.
61. Uechi, T., Tanaka, T. & Kenmochi, N. (2001) A complete map of the human ribosomal protein genes: assignment of 80 genes to the cytogenetic map and implications for human disorders. Genomics, 72, 223-230.
62. Waegele, J.W., Letsch, H., Klussmann-Kolb, A., Mayer, C., Misof, B. & Waegele, H. (2009) Phylogenetic support values are not necessarily informative: the case of the Serialia hypothesis (a mollusk phylogeny). Frontiers in Zoology, 6, 12.
63. Wilson, N.G., Rouse, G.W. & Giribet, G. (2009) Assessing the molluscan hypothesis Serialia (Monoplacophora+Polyplacophora) using novel molecular data. Molecular Phylogenetics and Evolution, 54, 187-193.
64. Winnepenninckx, B., Backeljau, T. & De Wachter, R. (1996) Investigation of molluscan phylogeny on the basis of 18S rRNA sequences. Molecular Biology and Evolution, 13, 1306-1317.
65. Wool, I., Chan, Y. & Gluck, A. (1995) Structure and evolution of mammalian ribosomal proteins. Biochemistry and Cell Biology, 73, 933-947.
66. Zhang, Z., Harrison, P. & Gerstein, M. (2002) Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Research, 12, 1466-1482.